polymerist.smileslib.chemdbqueries
==================================

.. py:module:: polymerist.smileslib.chemdbqueries

.. autoapi-nested-parse::

   For querying chemical databases for information about molecules specified by SMILES string and other structures



Attributes
----------

.. autoapisummary::

   polymerist.smileslib.chemdbqueries.LOGGER
   polymerist.smileslib.chemdbqueries.cirpy_error
   polymerist.smileslib.chemdbqueries.pubchempy_error


Exceptions
----------

.. autoapisummary::

   polymerist.smileslib.chemdbqueries.InvalidPropertyError
   polymerist.smileslib.chemdbqueries.NullPropertyResponse
   polymerist.smileslib.chemdbqueries.ChemicalDataQueryFailed


Classes
-------

.. autoapisummary::

   polymerist.smileslib.chemdbqueries.ChemDBServiceQueryStrategy
   polymerist.smileslib.chemdbqueries.NIHCACTUSQueryStrategy
   polymerist.smileslib.chemdbqueries.PubChemQueryStrategy


Functions
---------

.. autoapisummary::

   polymerist.smileslib.chemdbqueries.get_chemical_property


Module Contents
---------------

.. py:data:: LOGGER

.. py:exception:: InvalidPropertyError

   Bases: :py:obj:`Exception`


   Raised when attempting to query a property that a chemical database service cannot provide


.. py:exception:: NullPropertyResponse

   Bases: :py:obj:`Exception`


   Raised when a chemical database query doesn't fail BUT returns a NoneType where not allowed


.. py:exception:: ChemicalDataQueryFailed

   Bases: :py:obj:`Exception`


   Raised when a chemical data query is unfulfilled by a service


.. py:class:: ChemDBServiceQueryStrategy

   Bases: :py:obj:`abc.ABC`


   Implementation of queries from a particular chemical database


   .. py:method:: dependencies() -> Iterable[str]
      :classmethod:


      For internals, allows dynamic checking for package dependencies (useful for automating unit test boilerplate)



   .. py:method:: is_online() -> bool
      :classmethod:

      :abstractmethod:


      Check if the service being queried is online and can accept requests



   .. py:method:: queryable_properties() -> Container[str]
      :classmethod:

      :abstractmethod:


      List which chemical property names can be queried from the service



   .. py:method:: queryable_namespaces() -> Container[str]
      :classmethod:

      :abstractmethod:


      List which chemical identification types can be searched through by the service



   .. py:method:: validate_property(property_name: str) -> None

      Pre-check to ensure that a property is queryable from a service before attempting HTTP query



   .. py:method:: get_property(property_name: str, identifier: str, namespace: Optional[str], keep_first_only: bool = True, allow_null_return: bool = False, **kwargs) -> Optional[Any]

      Fetch a property associated with a molecule from a chemical database query service



.. py:data:: cirpy_error

.. py:class:: NIHCACTUSQueryStrategy

   Bases: :py:obj:`ChemDBServiceQueryStrategy`


   Implementation of chemical query requests to the NIH's CADD group
   Cheminformatics Tools and User Services (CACTUS) Chemical Identifier Resolver (CIR)


   .. py:attribute:: service_name
      :type:  ClassVar[str]
      :value: 'NIH CACTUS CIR'



   .. py:method:: dependencies()
      :classmethod:


      For internals, allows dynamic checking for package dependencies (useful for automating unit test boilerplate)



   .. py:method:: queryable_properties() -> set[str]
      :classmethod:


      List which chemical property names can be queried from the service



   .. py:method:: is_online()
      :classmethod:


      Check if the service being queried is online and can accept requests



   .. py:method:: queryable_namespaces() -> set[str]
      :classmethod:


      List which chemical identification types can be searched through by the service



.. py:data:: pubchempy_error

.. py:class:: PubChemQueryStrategy

   Bases: :py:obj:`ChemDBServiceQueryStrategy`


   Implementation of chemical query requests to PubChem via the
   PUG REST API (https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest)


   .. py:attribute:: service_name
      :type:  ClassVar[str]
      :value: 'PubChem'



   .. py:method:: dependencies()
      :classmethod:


      For internals, allows dynamic checking for package dependencies (useful for automating unit test boilerplate)



   .. py:method:: is_online()
      :classmethod:


      Check if the service being queried is online and can accept requests



   .. py:method:: queryable_properties() -> set[str]
      :classmethod:


      List which chemical property names can be queried from the service



   .. py:method:: queryable_namespaces() -> set[str]
      :classmethod:


      List which chemical identification types can be searched through by the service



.. py:function:: get_chemical_property(property_name: str, identifier: str, namespace: str = 'smiles', keep_first_only: bool = True, allow_null_return: bool = False, fail_quietly: bool = False, services: Optional[Sequence[ChemDBServiceQueryStrategy]] = None, **kwargs) -> Optional[Any]

   Attempt to fetch a molecular property from a variety of chemical database services, either
   provided manually (in the order they should be checked) or ALL implemented service queries by default

   Will return the first valid returned result or, if all services fail, raise Exception